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Xabier Vázquez-Campos, PhD
Computational biologist | Environmental microbiologist
Education
PhD in Environmental Engineering
The University of New South Wales
Sydney, Australia
2015 - 2011
MSc in Microbiology
Autonomous University of Madrid
Madrid, Spain
2008 - 2007
- Thesis: “Set-up of molecular ecology methodologies for the monitoring of microbial populations in an indirect reactor for the bioleaching of Zn from polymetallic sulfide concentrates” [in Spanish].
- Supervisor: Prof. Ricardo Amils.
Licenciate in Biology
University of Vigo
Vigo, Spain
2007 - 2002
- 5 years degree (300 ECTS).
- Equivalent to BSc in Biology and MSc in Biotechnology.
Research Experience
Research assistant (casual)
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Current - 2023
Bioinformatics scientist
MINIMUM bio
Sydney, Australia
2023
Visiting fellow
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
2023
Senior research associate / Postdoctoral fellow
NSW Systems Biology Initiative. School of Biotechnology and Biomolecular Sciences
The University of New South Wales
2022
- Bioinformatics support / consulting.
- Consulting for the Ramaciotti Centre for Genomics, and its customers, esp. amplicon, metagenomics and Oxford Nanopore applications.
Research associate / Postdoctoral fellow
NSW Systems Biology Initiative. School of Biotechnology and Biomolecular Sciences
The University of New South Wales
2021 - 2017
- Consulting for the Ramaciotti Centre for Genomics.
- Collaborative bioinformatics reasearch as part of a team including the users of the Ramaciotti Centre for genomics.
Research associate / Postdoctoral fellow
BioGEMS group. Water Research Centre and School of Civil and Environmental Engineering
The University of New South Wales
2017 - 2015
- Study of microbial communities in a burial ground containing mixed radioactive waste (Pu, Am).
- Metagenomics of and groundwater and soil. Reconstruction of microbial genomes from metagenomic data.
- Management of the PC2 microbiology laboratory and management support for the Radiation laboratory.
Research assistant (casual)
BioGEMS group, School of Civil and Environmental Engineering
The University of New South Wales
2011
Research assistant
Bioprocesses Group, Faculty of Chemistry
University of Vigo
2011 - 2010
- DRACORE project: DRAgado + COnfinamiento + REvalorización (Dredging + Containment + Revaluation).
- Testing of heavy metal resistance; testing of aliphatic and polycyclic hydrocarbons as sole carbon sources and biodegradation; HPLC operation; microorganism isolation;…
Research assistant
Bioprocesses Group, Faculty of Chemistry
University of Vigo
2007 - 2006
- Introduction to research grant from the Spanish Science and Education Ministry.
Teaching assistant
Faculty of Biology
University of Vigo
2006
- Lecturer’s support in the Bologna process.
- Grant provider: University of Vigo.
Teaching Experience
Courses
CVEN9855 - Water & Wastewater Analysis
School of Civil and Environmental Engineering.
The University of New South Wales
2020
- Term 1. Section on microbiology of wastewater
Invited lectures
Uranium heap leaching: Microbiological aspects
School of Civil and Environmental Engineering.
The University of New South Wales
2012
Workshops
EMBL-ABR: Phylogenetic trees for beginners
EMBL-ABR (Sydney node).
The University of New South Wales
2019
- Node organiser and facilitator.
EMBL-ABR: Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow
EMBL-ABR (Sydney node).
The University of New South Wales
N/A
- Facilitator.
EMBL-ABR: 16S Metagenomics with Galaxy Australia
EMBL-ABR (Sydney node).
University of Sydney
2018
- Facilitator.
Long-read Data Analysis Workshop
NSW Systems Biology Initiative.
The University of New South Wales
N/A
- Organiser, trainer, facilitator.
Hands on Zotero, a free alternative to EndNote
Bioprocesses group.
University of Vigo
2011
- Organiser, sole trainer.
- Group’s internal workshop.
Supervision
Kevin Yonathan
PhD. Role: External supervisor.
University of Technology, Sydney
Current - 2019
Study of the response of microbial communities to silver nanoparticles through metagenomics.
I have also informally supervised, supported, mentored, or collaborated with a total of 21 students across multiple levels (1 Course project, 7 Honours, 12 PhD, and 1 Practicum).
Grants
BABS sequencing grant
Investigation of a phage capable of species cross-infection
School of Biotechnology and Biomolecular Sciences / Ramaciotti Centre for Genomics at
The University of New South Wales
2020
- AU$5,000 for sequencing
- Role: co-CI with Dr. Dragica Damnjanović and Dr. Melissa Harvey
ResTech Support Scheme
OTUreporter pipeline coding project
The University of New South Wales
2020 - 2019
- AU$15,000
- Role: project lead. CI: Prof. Marc Wilkins
Postdoctoral writing Fellowship Grant
N/A
School of Civil and Environmental Engineering at The University of New South Wales
2015
- 0.4 FTE salary for 12 weeks
UNSW Tuition fee scholarship
N/A
Graduate Research School at The University of New South Wales
2015 - 2011
- Tuition fees for PhD program
- Supervisors: Prof. T. David Waite and Prof. Brett A. Neilan
Australian Postgraduate Award (Industry)
N/A
Australian Federal Government
2015 - 2011
- AU$27,651.00 per year for 3.5 years
- Supervisors: Prof. T. David Waite and Prof. Brett A. Neilan
Awards
SRAP Laureate 2020
N/A
Spanish Researchers in Australia-Pacific
2020
Training and professional development
I have completed about 90 h of training in courses and workshops in the last two years alone.
Courses
Differential Expression Analysis with limma in R
DataCamp.
Online
2022
R Programming - Skill Track (updated)
DataCamp.
Online
N/A
Importing & Cleaning Data with R - Skill Track
DataCamp.
Online
N/A
Data manipulation with R - Skill Track
DataCamp.
Online
N/A
Data Visualization with R - Skill Track
DataCamp.
Online
N/A
Intermediate Tidyverse Toolbox Track - Skill Track
DataCamp.
Online
2021
SQL Fundamentals - Skill Track
DataCamp.
Online
2020
R Programming - Skill Track
DataCamp.
Online
N/A
Python Fundamentals - Skill Track
DataCamp.
Online
N/A
Tidyverse Fundamentals with R - Skill Track
DataCamp.
Online
N/A
Introduction to Git for Data Science
DataCamp.
Online
2018
Jekyll: make fast, secure static sites and blogs with Jekyll
Udemy.
Online
N/A
Introduction to Python for Data Science (DAT208x)
Microsoft.
Online
2016
Introduction to R for Data Science (DAT204x)
Microsoft.
Online
N/A
Astrobiology and the Search for Extraterrestrial Life
The University of Edinburgh.
Online
2015
HTML & CSS
Codecademy.
Online
N/A
Introduction to Genomic Technologies
Johns Hopkins University.
Online
N/A
Workshops
Using containers in bioinformatics
Australia BioCommons.
Remote
N/A
Path Forward for Naming the Uncultivated
SeqCode2021 committee.
Remote
N/A
JAMS 2018 TOAST Workshop
Joint Academic Microbiology Seminars.
University of Technology, Sydney, AUS
2018
Resolving Microbial Communities At Strain-Level Resolution
A. Murat Eren et al..
University of Exeter, GBR
N/A
Genome annotation using Apollo
Monica Munoz-Torres / EMBL-ABR.
Remote
2017
The Omics Analysis Sydney Tutorial (TOAST)
Joint Academic Microbiology Seminars.
Australian Museum, Sydney, AUS
2016
Anvi’o workshop
A. Murat Eren et al..
University of Montreal, CAN
N/A
Bioinformatics for microbial ecology and genomics
Australian Society for Microbiology.
Australia National University, Canberra, AUS
2015
Publications
Under review
Effect of standardized ginger root powder on gastrointestinal bacteria composition, gastrointestinal symptoms, mental health, fatigue, and quality of life: A double-blind placebo-controlled trial
Journal of the Academy of Nutrition and Dietetics, JANDJRL-S-22-00854.
N/A
2022
M. Crichton, S. Marshall, W. Marx, E. Isenring, X. Vázquez-Campos, S. L. Dawson & A. Lohning.
Journal articles
Cross-linking mass spectrometry discovers, evaluates, and corroborates structures and protein–protein interactions in the human cell
Proceedings of the National Academy of Sciences 120(17), e2219418120.
N/A
2023
T. K. Bartolec, X. Vázquez-Campos, A. Norman, C. Luong, M. Johnson, R. J. Payne, M. R. Wilkins, J. P. Mackay & J. K. Low.
Evidence for a putative isoprene reductase in Acetobacterium wieringae
N/A
N/A
M. Kronen, X. Vázquez-Campos, M. R. Wilkins, M. Lee & M. J. Manefield.
Contaminant release, mixing and microbial fluctuations initiated by infiltrating water within a replica field-scale legacy radioactive waste trench
Science of The Total Environment 851(Part 1), 158241.
N/A
2022
A. S. Kinsela, T. E. Payne, M. W. Bligh, X. Vázquez-Campos, M. R. Wilkins, M. J. Comarmond, B. Rowling & T. D. Waite.
Metaproteomics reveals methyltransferases implicated in dichloromethane and glycine betaine fermentation by ‘Candidatus Formimonas warabiya’ strain DCMF
Frontiers in Microbiology 13, 1035247.
N/A
N/A
S. I. Holland, X. Vázquez-Campos, E. Haluk, R. J. Edwards, M. J. Manefield & M. Lee.
The interplay between use of biological therapies, psychological state, and the microbiome in IBD
Frontiers in Medicine 9, 788992.
N/A
N/A
P. Tavakoli, U. Vollmer-Conna, D. Hadzi-Pavlovic, X. Vázquez-Campos & M. C. Grimm.
Characterisation of bacteriophage vB_SmaM_Ps15 infective to Stenotrophomonas maltophilia clinical ocular isolates
N/A
N/A
D. Damnjanović, X. Vázquez-Campos, L. Elliot, M. Willcox & W. J. Bridge.
Genomic insights into the Archaea inhabiting an Australian radioactive legacy site
Frontiers in Microbiology 12, 732575.
N/A
2021
X. Vázquez-Campos, A. S. Kinsela, M. W. Bligh, T. E. Payne, M. R. Wilkins & T. D. Waite.
Biogeochemical mobility of contaminants from a replica radioactive waste trench in response to rainfall-induced redox oscillations
Environmental Science & Technology 55(13), 8793-8805.
N/A
N/A
A. S. Kinsela, M. W. Bligh, X. Vázquez-Campos, Y. Sun, M. R. Wilkins, M. J. Comarmond, B. Rowling, T. E. Payne & T. D. Waite.
Biocrust cyanobacterial composition, diversity, and environmental drivers in two contrasting climatic regions in Brazil
N/A
N/A
N. M. Machado de Lima, M. Muñoz-Rojas, X. Vázquez-Campos & L. H. Branco.
Community-led, integrated, reproducible multi-omics with anvi’o
Nature Microbiology 6(1), 3-6.
N/A
N/A
A. M. Eren, E. Kiefl, A. Shaiber, I. Veseli, S. E. Miller, M. S. Schechter, I. Fink, J. N. Pan, M. Yousef, E. C. Fogarty, F. Trigodet, A. R. Watson, Ö. C. Esen, R. M. Moore, Q. Clayssen, M. D. Lee, V. Kivenson, E. D. Graham, B. D. Merrill, A. Karkman, D. Blankenberg, J. M. Eppley, A. Sjödin, J. J. Scott, X. Vázquez-Campos, L. J. McKay, E. A. McDaniel, S. L. Stevens, R. E. Anderson, J. Fuessel, A. Fernandez-Guerra, L. Maignien, T. O. Delmont & A. D. Willis.
Shed Light in the DaRk LineagES of the Fungal Tree of Life—STRES
N/A
2020
L. Selbmann, Z. Benkő, C. Coleine, S. de Hoog, C. Donati, I. Druzhinina, T. Emri, C. L. Ettinger, A. S. Gladfelter, A. A. Gorbushina, I. V. Grigoriev, M. Grube, N. Gunde-Cimerman, Z. Á. Karányi, B. Kocsis, T. Kubressoian, I. Miklós, M. Miskei, L. Muggia, T. Northen, M. Novak-Babič, C. Pennacchio, W. P. Pfliegler, I. Pòcsi, V. Prigione, M. Riquelme, N. Segata, J. Schumacher, E. Shelest, K. Sterflinger, D. Tesei, J. M. U’Ren, G. C. Varese, X. Vázquez-Campos, V. A. Vicente, E. M. Souza, P. Zalar, A. K. Walker & J. E. Stajich.
Bacteriophage genotyping using BOXA repetitive-PCR
N/A
N/A
D. Damnjanovic, X. Vázquez-Campos, D. L. Winter, M. Harvey & W. J. Bridge.
Disentangling the drivers of functional complexity at the metagenomic level in Shark Bay microbial mat microbiomes
The ISME Journal 12, 2619-2639.
N/A
2018
H. L. Wong, R. A. White III, P. T. Visscher, J. C. Charlesworth, X. Vázquez-Campos & B. P. Burns.
Response of microbial community function to fluctuating geochemical conditions within a legacy radioactive waste trench environment
Applied and Environmental Microbiology 83(17), e00729.
N/A
2017
X. Vázquez-Campos, A. S. Kinsela, M. Bligh, J. J. Harrison, T. E. Payne & T. D. Waite.
Uranium extraction from a low-grade, stockpiled, non-sulfidic ore: Impact of added iron and the native microbial consortia
N/A
N/A
X. Vázquez-Campos, A. S. Kinsela, R. N. Collins, B. A. Neilan & T. D. Waite.
Uranium binding mechanisms of the acid-tolerant fungus Coniochaeta fodinicola
Environmental Science & Technology 49(14), 8487-8496.
N/A
2015
X. Vázquez-Campos, A. S. Kinsela, R. N. Collins, B. A. Neilan, N. Aoyagi & T. D. Waite.
Acidotolerant genus Fodinomyces (Ascomycota: Capnodiales) is a synonym of Acidiella
N/A
N/A
M. Kolařík, M. Hujslová & X. Vázquez-Campos.
Fodinomyces uranophilus gen. nov. sp. nov. and Coniochaeta fodinicola sp. nov., two uranium mine inhabiting Ascomycota fungi from northern Australia
N/A
2014
X. Vázquez-Campos, A. S. Kinsela, T. D. Waite, R. N. Collins & B. A. Neilan.
Technical Reports
A WHO collaborative study to evaluate the candidate 1st WHO International Reference Reagents for Gut Microbiome analysis by Next-Generation Sequencing
C. Sergaki, S. Anwar, J. Hassall, A. Logan, P. Rigsby, S. Rijpkema, G. Amos & . study participants. WHO Publication, p. 63.
N/A
2022
Biogeochemical controls of uranium heap leaching
A. Kinsela, X. Vázquez-Campos, R. Collins, B. Neilan & T. Waite. Project Completion Report to ERA, p. 87.
N/A
2015
Conference contributions
Oral presentations
Unusual DPANN Archaea from a radioactive legacy site
Australian Microbial Ecology Conference (AusME 2019).
Perth, WA, Australia
2019
X. Vázquez-Campos, A. S. Kinsela, M. W. Bligh, M. R. Wilkins, T. E. Payne & T. D. Waite.
Posters
OTUreporter: amplicon to report in a single command
Joint 30th International Conference on Genome Informatics (GIW) & Australian Bioinformatics and Computational Biology Society (ABACBS) Annual Conference (GIW/ABACBS 2019).
Sydney, NSW, Australia
2019
X. Vázquez-Campos, D. McFarlane, A. M. Chilton, J. R. Koval & M. R. Wilkins.
OTUreporter: an automated pipeline for the analysis and report of amplicon sequencing data
ABACBS-2018 National Conference.
Melbourne, VIC, Australia
2018
X. Vázquez-Campos, A. Chilton, J. Koval, J. J. Tree & M. R. Wilkins.
New Archaea lineages from a radioactive legacy site
Molecular biology of archaea: From mechanisms to ecology (MoBA6).
Vienna, Austria
N/A
X. Vázquez-Campos, A. S. Kinsela, M. W. Bligh, M. R. Wilkins, T. E. Payne & T. D. Waite.
OTUreporter: a modular automated pipeline for the analysis and report of amplicon data
Sydney Bioinformatics Research Symposium 2018.
Sydney, NSW, Australia
N/A
X. Vázquez-Campos, A. Chilton, J. Koval, J. J. Tree & M. R. Wilkins.
Phylogenomics of a radioactive legacy site reveals new Archaea phyla of unknown function
Sydney Bioinformatics Research Symposium 2017.
Sydney, NSW, Australia
2017
X. Vázquez-Campos, A. S. Kinsela, M. R. Wilkins, T. E. Payne & T. D. Waite.
Rainfall-mediated biogeochemical changes at a legacy radionuclide waste disposal site
16th International Symposium on Microbial Ecology (ISME16).
Montreal, Canada
2016
X. Vázquez-Campos, A. S. Kinsela, J. J. Harrison, K. Wilsher, S. Thiruvoth, B. Rowling, T. E. Payne & T. D. Waite.
Biogeochemical changes during experimental column leaching of a weathered uranium composite
15th International Symposium on Microbial Ecology (ISME15).
Seoul, South Korea
2014
X. Vázquez-Campos, A. Kinsela, T. Waite, R. Collins & B. Neilan.
Co-authored contributions
Contributed abstracts presented by co-authors at conferences. Showing selected 5 out of 27.
Exploring the human structural proteome, complexome and interactome with deep, large-scale crosslinking mass spectrometry
27th Annual Lorne Proteomics Symposium.
Lorne, VIC, Australia
2022
T. K. Bartolec, M. Johnson, A. Hawken, A. Norman, R. J. Payne, X. Vázquez-Campos, M. R. Wilkins, J. P. Mackay & J. K. Low.
Nanosilver in the aquatic environment: impact on microbial communities
22nd EMBL PhD Symposium “The Roaring 20s: A New Decade for Life Sciences”.
EMBL Heidelberg, Germany
2020
K. Yonathan, X. Vázquez-Campos, R. Mann, K. R. Mahbub & C. Gunawan.
The impact of repeated redox cycling events on the biogeochemistry of a simulated legacy radioactive waste trench
17th International Conference on the Chemistry and Migration Behaviour of Actinides and Fission Products in the Geosphere.
Kyoto, Japan
2019
A. S. Kinsela, M. W. Bligh, X. Vázquez-Campos, T. D. Waite, T. E. Payne, M. J. Comarmond & B. Rowling.
Microbial profiling of the Himalayan Puga geothermal system: towards an astrobiological model
Astrobiology Australasia Conference 2018.
Rotorua, New Zealand
2018
A. M. Chilton, X. Vázquez-Campos, L. Steller, T. Djokic & M. J. Van Kranendonk.
Understanding oat stem rust pathogen genome by PacBio sequencing
Sydney Bioinformatics Research Symposium 2017.
Sydney, NSW, Australia
2017
C. Dong, X. Vázquez-Campos, N. Deshpande, P. Zhang, M. R. Wilkins & R. F. Park.
Invited talks
Current trends in academia: online presence, community service and openness
Water Research Centre research seminar series.
Water Research Centre, Kensington, Australia
2019
Assembly and annotation of Puccinia graminis f. sp. avenae, ‘oat stem rust’. Lessons about the process and some results
Invited talk at the Plant Breeding Institute.
Plant Breeding Institute, Cobbitty, Australia
2017
Service
Institutional Service
- University of New South Wales
- Postgraduate student representative at the OH&S Committee of the School of Civil and Environmental Engineering (2013–2015).
N/A
Professional Affiliations
- American Society for Microbiology
- Regular member (2015–Current).
- Australian Bioinformatics and Computational Biology Society
- Regular member (2018–Current).
- Australian Society for Microbiology
- Regular member (2015–Current).
- International Society for Microbial Ecology
- Regular member (2014–Current).
- Spanish Researchers in Australia-Pacific
- Co-founder (2014).
- Board member and web/IT coordinator (2014–2020).
- Regular member (2021–Current).
N/A
Conferences
- Australian Microbial Ecology conference 2022 (AusME2022)
- Plenary chair and poster judge (2022).
- 6th Australia-Spain Research Forum: Big Data
- Event registration (2020).
- 5th Australia-Spain Research Forum: 5 years Bridging Australia and Spain in Research and Academia
- Website (2019).
- 4th Australia-Spain Research Forum: Earth
- Website (2018).
- 3rd Australia-Spain Research Forum: Air
- Website and event registration (2017).
- 2nd Australia-Spain Research Forum: Light
- Website (2016).
- Australia-Spain Water Forum
- Website and event photography (2015).
N/A
Peer Reviews
Reviewer for >10 different journals since 2016, including leading journals in their own fields, e.g., Astrobiology, Environmental Science and Technology, or Microbiome.
N/A
N/A
For a full record as reviewer, consult my public ResearcherID profile.